Table 2.

Overview of the TRITEX pipeline

	Step1	Software	Input	Output
1	Read merging	BBMerge [25]	PE450 read pairs	Merged PE450 reads
2	PE450 error correction	BFC [26]	Merged PE450 reads	Corrected PE450 reads, hash table of k-mer counts
3.1	Unitig assembly	Minia3 [27, 28]	Corrected PE450 reads	Unitigs
3.2	Error correction of PE800 and MP reads	BFC [26], cutadapt [29], NxTrim [30]	PE800, MP3, MP6, and MP9 reads, hash table of k-mer count (step 2)	Corrected PE800, MP3, MP6, and MP9 reads
4	Scaffolding	SOAPDenovo2 [31]	Unitigs; corrected PE800, MP3, MP6, and MP9 reads	Scaffolds
5	Gap-filling	Gapcloser [31]	Scaffolds, corrected PE450 reads	Scaffolds after gap-filling
6.1	Alignment of 10X reads	Minimap2 [32], cutadapt [29], SAMtools [33], BEDtools [34], custom scripts	Scaffolds after gap-filling, 10X reads	10X alignment records
6.2	Alignment of Hi-C reads	As in 6.1, EMBOSS [35]	Scaffolds after gap-filling, Hi-C reads	Hi-C alignment records
6.3	Alignment of genetic markers	Minimap2 [32]	Scaffolds after gap-filling, marker sequences	Marker alignment records
7	Pseudomolecule construction	Custom R scripts	Scaffolds after gap-filling, 10X alignment records, Hi-C alignment records, marker alignment records	Pseudomolecules, Hi-C contact maps

¹Steps with identical leading digits can be run in parallel